Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

Awesome, thanks for the quick fix! > On Nov 3, 2016, at 14:50, Hervé Pagès wrote: > > Should now be fixed in release (GenomeInfoDb 1.10.1) and devel > (GenomeInfoDb 1.11.2). > > H. > > On 11/03/2016 11:12 AM, Hervé Pagès wrote: >> I'll look at this. I think

Re: [R-pkg-devel] Orphaned Package listing trouble?

On Thu, 2016-11-03 at 18:38 +0100, Uwe Ligges wrote: > > On 03.11.2016 18:20, Joseph Stachelek wrote: > > > > Hello all, > > > > I am interested in updating a CRAN package which has the primary > > purpose of serving a particular government database. This package > > has > > seen no activity

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

Should now be fixed in release (GenomeInfoDb 1.10.1) and devel (GenomeInfoDb 1.11.2). H. On 11/03/2016 11:12 AM, Hervé Pagès wrote: I'll look at this. I think Seqinfo(genome="hg19") needs to query NCBI to get some information (e.g. SequenceRole) that allows ordering the sequences in the

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

I'll look at this. I think Seqinfo(genome="hg19") needs to query NCBI to get some information (e.g. SequenceRole) that allows ordering the sequences in the returned Seqinfo in the "natural" order. H. On 11/03/2016 05:47 AM, Michael Lawrence wrote: I think this is because the NCBI server

Re: [R-pkg-devel] Orphaned Package listing trouble?

For the orphaned package list, search for "Orphaned" in https://cran.r-project.org/src/contrib/PACKAGES.in Gabor On Thu, Nov 3, 2016 at 5:20 PM, Joseph Stachelek wrote: > Hello all, > > I am interested in updating a CRAN package which has the primary > purpose of serving a

Re: [R-pkg-devel] Orphaned Package listing trouble?

On 03.11.2016 18:20, Joseph Stachelek wrote: Hello all, I am interested in updating a CRAN package which has the primary purpose of serving a particular government database. This package has seen no activity since 2014 and is now out-of-date. I have contacted the maintainer email (waited

Re: [Rd] Running package tests and not stop on first fail

Hi Martin, Jan, On 11/03/2016 03:45 AM, Martin Maechler wrote: Jan Gorecki on Tue, 1 Nov 2016 22:51:28 + writes: > Hello community/devs, Is there an option to run package > tests during R CMD check and not stop on first error? I > know that testing

Re: [Bioc-devel] What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation

Links to those Bioc Views: - http://bioconductor.org/packages/devel/BiocViews.html#___MethylSeq - http://bioconductor.org/packages/devel/BiocViews.html#___DNAMethylation - http://bioconductor.org/packages/devel/BiocViews.html#___DifferentialMethylation 2016-11-03 16:56 GMT+01:00

[Bioc-devel] What are the differences between Bioc Views: MethylSeq, DNAMethylation and DifferentialMethylation

Dear Bioc devs, I am looking for a tool to jointly analyze methylation and expression data from TCGA. As I haven't earlier used R for finding differentially methylated bases or regions I thought Bioc Views would be a great start to look for the tool to analyze the methylation data. I am

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

I think this is because the NCBI server switched to https (via a redirect that I guess the R url() connection fails to follow). The reason rtracklayer still works is that it's only querying UCSC. GenomeInfoDb also queries NCBI to get the mappings to the NCBI seqlevels. Does that really need to

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

> GenomeInfoDb::Seqinfo(genome='hg19') Error in file(file, "rt") : cannot open the connection > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin15.5.0 (64-bit) Running under: OS X 10.12.1 (Sierra) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

Re: [Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

sessionInfo()? On Thu, Nov 3, 2016 at 5:13 AM, Raymond Cavalcante wrote: > Hello, > > Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19') > stopped working with the error: > > > Error in file(file, "rt") : cannot open the connection > > From the

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

Apologies for the additional spam, for two reasons: - The diff files that I've previously sent had the base and modified versions swapped. This new one fixes that. - This new diff file (always relative to the code I cloned from Bioconductor-mirror) also fixes a bug whereby the updated

[Bioc-devel] GenomeInfoDb::Seqinfo(genome) broken?

Hello, Sometime yesterday calls like GenomeInfoDb::Seqinfo(genome = 'hg19') stopped working with the error: > Error in file(file, "rt") : cannot open the connection From the documentation, that call relies on fetchExtendedChromInfoFromUCSC() and requires an internet connection, which I had

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

Hi all, Please find attached the diff relative to the code that I cloned from Bioconductor-mirror yesterday (please ignore the previous diff file). Basically three new features: - As per previous email: display up to the first 6 lines that are over 80 characters long - *New*: display

Re: [Rd] Running package tests and not stop on first fail

> Jan Gorecki > on Tue, 1 Nov 2016 22:51:28 + writes: > Hello community/devs, Is there an option to run package > tests during R CMD check and not stop on first error? I > know that testing frameworks (testhat and others) can do > that but

[Rd] .S4methods inconsistent behavior with methods, .S3methods

If I call .S4methods(sd) I get the error ## Error in getGeneric(generic.function) : ## argument 'f' must be a string, generic function, or primitive: got an ordinary function By contrast, methods and .S3methods just state that no methods are found. methods(sd) ## no methods found